Author: pbenner-guest Date: 2009-01-25 23:18:23 +0000 (Sun, 25 Jan 2009) New Revision: 3055
Added: trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch trunk/packages/wise/trunk/debian/patches/02_isnumber.patch trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch trunk/packages/wise/trunk/debian/patches/series Removed: trunk/packages/wise/trunk/debian/patches/00list trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch Modified: trunk/packages/wise/trunk/debian/changelog trunk/packages/wise/trunk/debian/control trunk/packages/wise/trunk/debian/rules Log: using quilt instead of dpatch Modified: trunk/packages/wise/trunk/debian/changelog =================================================================== --- trunk/packages/wise/trunk/debian/changelog 2009-01-25 09:02:24 UTC (rev 3054) +++ trunk/packages/wise/trunk/debian/changelog 2009-01-25 23:18:23 UTC (rev 3055) @@ -1,10 +1,12 @@ -wise (2.4.1-6) UNRELEASED; urgency=low +wise (2.4.1-6) unstable; urgency=low - [debian/control] - * Updated policy to 3.8.0 (no changes required) - * wise now suggests wise-doc (downgraded from 'recommends') + * Updated policy to 3.8.0 (no changes required). + * wise now suggests wise-doc (downgraded from 'recommends'). + [ Steffen Moeller ] + * Using quilt instead of dpatch. + [ Philipp Benner ] - -- Steffen Moeller <[email protected]> Sun, 28 Dec 2008 14:00:29 +0100 + -- Philipp Benner <[email protected]> Sun, 25 Jan 2009 22:57:27 +0000 wise (2.4.1-5) unstable; urgency=low Modified: trunk/packages/wise/trunk/debian/control =================================================================== --- trunk/packages/wise/trunk/debian/control 2009-01-25 09:02:24 UTC (rev 3054) +++ trunk/packages/wise/trunk/debian/control 2009-01-25 23:18:23 UTC (rev 3055) @@ -4,9 +4,9 @@ Maintainer: Debian-Med Packaging Team <[email protected]> Uploaders: Philipp Benner <[email protected]> DM-Upload-Allowed: yes -Build-Depends: debhelper (>= 5), dpatch (>= 2.0.21), texlive-latex-base, +Build-Depends: debhelper (>= 5), quilt, texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib1.2-dev -Standards-Version: 3.7.3 +Standards-Version: 3.8.0 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wise/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/wise/trunk/ Homepage: http://www.ebi.ac.uk/~birney/wise2/ Deleted: trunk/packages/wise/trunk/debian/patches/00list =================================================================== --- trunk/packages/wise/trunk/debian/patches/00list 2009-01-25 09:02:24 UTC (rev 3054) +++ trunk/packages/wise/trunk/debian/patches/00list 2009-01-25 23:18:23 UTC (rev 3055) @@ -1,4 +0,0 @@ -01_welcome-csh -02_isnumber -03_doc-nodycache -04_wise2-pdflatex-update Deleted: trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch =================================================================== --- trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch 2009-01-25 09:02:24 UTC (rev 3054) +++ trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch 2009-01-25 23:18:23 UTC (rev 3055) @@ -1,28 +0,0 @@ -#! /bin/sh /usr/share/dpatch/dpatch-run -## 01_welcome-csh.dpatch by Philipp Benner <[email protected]> -## -## All lines beginning with `## DP:' are a description of the patch. -## DP: No description. - -...@dpatch@ -diff -urNad wise-2.4.0~/src/makefile wise-2.4.0/src/makefile ---- wise-2.4.0~/src/makefile 2007-07-15 23:39:24.000000000 +0200 -+++ wise-2.4.0/src/makefile 2007-07-15 23:41:11.000000000 +0200 -@@ -109,7 +109,7 @@ - bin : - mkdir bin - cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin -- csh welcome.csh -+ ./welcome.csh - - libs : - (cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a ) -diff -urNad wise-2.4.0~/src/welcome.csh wise-2.4.0/src/welcome.csh ---- wise-2.4.0~/src/welcome.csh 2007-07-15 23:39:24.000000000 +0200 -+++ wise-2.4.0/src/welcome.csh 2007-07-15 23:40:46.000000000 +0200 -@@ -1,4 +1,4 @@ --#!/bin/tcsh -f -+#!/bin/sh - - echo "" - echo "Welcome to Wise2.4" Copied: trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch (from rev 3054, trunk/packages/wise/trunk/debian/patches/01_welcome-csh.dpatch) =================================================================== --- trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch (rev 0) +++ trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch 2009-01-25 23:18:23 UTC (rev 3055) @@ -0,0 +1,28 @@ +#! /bin/sh /usr/share/dpatch/dpatch-run +## 01_welcome-csh.dpatch by Philipp Benner <[email protected]> +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: No description. + +...@dpatch@ +diff -urNad wise-2.4.0~/src/makefile wise-2.4.0/src/makefile +--- wise-2.4.0~/src/makefile 2007-07-15 23:39:24.000000000 +0200 ++++ wise-2.4.0/src/makefile 2007-07-15 23:41:11.000000000 +0200 +@@ -109,7 +109,7 @@ + bin : + mkdir bin + cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin +- csh welcome.csh ++ ./welcome.csh + + libs : + (cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a ) +diff -urNad wise-2.4.0~/src/welcome.csh wise-2.4.0/src/welcome.csh +--- wise-2.4.0~/src/welcome.csh 2007-07-15 23:39:24.000000000 +0200 ++++ wise-2.4.0/src/welcome.csh 2007-07-15 23:40:46.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/bin/tcsh -f ++#!/bin/sh + + echo "" + echo "Welcome to Wise2.4" Property changes on: trunk/packages/wise/trunk/debian/patches/01_welcome-csh.patch ___________________________________________________________________ Name: svn:executable + * Name: svn:mergeinfo + Deleted: trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch =================================================================== --- trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch 2009-01-25 09:02:24 UTC (rev 3054) +++ trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch 2009-01-25 23:18:23 UTC (rev 3055) @@ -1,18 +0,0 @@ -#! /bin/sh /usr/share/dpatch/dpatch-run -## 02_isnumber.dpatch by Philipp Benner <[email protected]> -## -## DP: Replace isnumber() (which does not exist on linux) by isdigit(). - -...@dpatch@ -diff -urNad wise-2.4.0~/src/models/phasemodel.c wise-2.4.0/src/models/phasemodel.c ---- wise-2.4.0~/src/models/phasemodel.c 2007-07-01 22:44:39.000000000 +0200 -+++ wise-2.4.0/src/models/phasemodel.c 2007-07-16 00:24:16.000000000 +0200 -@@ -20,7 +20,7 @@ - if( line[0] == '#' ) { - continue; - } -- if( !isnumber(line[0]) ) { -+ if( !isdigit(line[0]) ) { - warn("Bad looking line in intron file, %s",line); - continue; - } Copied: trunk/packages/wise/trunk/debian/patches/02_isnumber.patch (from rev 3054, trunk/packages/wise/trunk/debian/patches/02_isnumber.dpatch) =================================================================== --- trunk/packages/wise/trunk/debian/patches/02_isnumber.patch (rev 0) +++ trunk/packages/wise/trunk/debian/patches/02_isnumber.patch 2009-01-25 23:18:23 UTC (rev 3055) @@ -0,0 +1,18 @@ +#! /bin/sh /usr/share/dpatch/dpatch-run +## 02_isnumber.dpatch by Philipp Benner <[email protected]> +## +## DP: Replace isnumber() (which does not exist on linux) by isdigit(). + +...@dpatch@ +diff -urNad wise-2.4.0~/src/models/phasemodel.c wise-2.4.0/src/models/phasemodel.c +--- wise-2.4.0~/src/models/phasemodel.c 2007-07-01 22:44:39.000000000 +0200 ++++ wise-2.4.0/src/models/phasemodel.c 2007-07-16 00:24:16.000000000 +0200 +@@ -20,7 +20,7 @@ + if( line[0] == '#' ) { + continue; + } +- if( !isnumber(line[0]) ) { ++ if( !isdigit(line[0]) ) { + warn("Bad looking line in intron file, %s",line); + continue; + } Property changes on: trunk/packages/wise/trunk/debian/patches/02_isnumber.patch ___________________________________________________________________ Name: svn:executable + * Name: svn:mergeinfo + Deleted: trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch =================================================================== --- trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch 2009-01-25 09:02:24 UTC (rev 3054) +++ trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch 2009-01-25 23:18:23 UTC (rev 3055) @@ -1,19 +0,0 @@ -#! /bin/sh /usr/share/dpatch/dpatch-run -## 03_doc-nodycache.dpatch by Philipp Benner <[email protected]> -## -## DP: Documentation bugfix. - -...@dpatch@ -diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex ---- wise-2.4.0~/docs/wise2.tex 2003-03-26 12:47:08.000000000 +0100 -+++ wise-2.4.0/docs/wise2.tex 2007-07-16 01:05:34.000000000 +0200 -@@ -1617,7 +1617,8 @@ - \item[-hithelp] more detailed help on hitlist formats - \item[-dymem] memory style [default/linear/explicit] - \item[-kbyte] memory amount to use [4000] --\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes) -+\item[-dycache] implicitly cache dy matrix usage (default) -+\item[-nodycache] do not implicitly cache dy matrix usage - \item[-dydebug] drop into dynamite dp matrix debugger - \item[-paldebug] print PackAln after debugger run if used - \item[-help] show help options Copied: trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch (from rev 3054, trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.dpatch) =================================================================== --- trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch (rev 0) +++ trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch 2009-01-25 23:18:23 UTC (rev 3055) @@ -0,0 +1,19 @@ +#! /bin/sh /usr/share/dpatch/dpatch-run +## 03_doc-nodycache.dpatch by Philipp Benner <[email protected]> +## +## DP: Documentation bugfix. + +...@dpatch@ +diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex +--- wise-2.4.0~/docs/wise2.tex 2003-03-26 12:47:08.000000000 +0100 ++++ wise-2.4.0/docs/wise2.tex 2007-07-16 01:05:34.000000000 +0200 +@@ -1617,7 +1617,8 @@ + \item[-hithelp] more detailed help on hitlist formats + \item[-dymem] memory style [default/linear/explicit] + \item[-kbyte] memory amount to use [4000] +-\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes) ++\item[-dycache] implicitly cache dy matrix usage (default) ++\item[-nodycache] do not implicitly cache dy matrix usage + \item[-dydebug] drop into dynamite dp matrix debugger + \item[-paldebug] print PackAln after debugger run if used + \item[-help] show help options Property changes on: trunk/packages/wise/trunk/debian/patches/03_doc-nodycache.patch ___________________________________________________________________ Name: svn:executable + * Name: svn:mergeinfo + Deleted: trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch =================================================================== --- trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch 2009-01-25 09:02:24 UTC (rev 3054) +++ trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch 2009-01-25 23:18:23 UTC (rev 3055) @@ -1,43 +0,0 @@ -#! /bin/sh /usr/share/dpatch/dpatch-run -## 04_wise2-pdflatex-update.dpatch by Philipp Benner <[email protected]> -## -## DP: Make wise2.tex pdflatex compatible. - -...@dpatch@ - -diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex ---- wise-2.4.0~/docs/wise2.tex 2007-08-06 10:25:05.000000000 +0200 -+++ wise-2.4.0/docs/wise2.tex 2007-08-06 10:25:08.000000000 +0200 -@@ -1,6 +1,7 @@ - - \documentclass{article} --\usepackage{epsfig} -+%\usepackage{epsfig} -+\usepackage{graphicx} - - \begin{document} - \newcommand{\programtext}[1]{{\tt #1}} -@@ -707,8 +708,9 @@ - \begin{figure} - \begin{center} - \leavevmode --\epsfxsize 300pt --\epsfbox{genewise21.eps} -+%\epsfxsize 300pt -+%\epsfbox{genewise21.eps} -+%\includegraphics[scale=0.75]{genewise21.pdf} - \newline - \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the - arrows between them transitions. Black transitions are standard -@@ -898,8 +900,9 @@ - \begin{figure} - \begin{center} - \leavevmode --\epsfxsize 300pt --\epsfbox{genewise6.eps} -+%\epsfxsize 300pt -+%\epsfbox{genewise6.eps} -+%\includegraphics[scale=0.75]{genewise6.pdf} - \newline - \caption{GeneWise6:23} - \label{Figure:genewise623} Copied: trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch (from rev 3054, trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.dpatch) =================================================================== --- trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch (rev 0) +++ trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch 2009-01-25 23:18:23 UTC (rev 3055) @@ -0,0 +1,43 @@ +#! /bin/sh /usr/share/dpatch/dpatch-run +## 04_wise2-pdflatex-update.dpatch by Philipp Benner <[email protected]> +## +## DP: Make wise2.tex pdflatex compatible. + +...@dpatch@ + +diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex +--- wise-2.4.0~/docs/wise2.tex 2007-08-06 10:25:05.000000000 +0200 ++++ wise-2.4.0/docs/wise2.tex 2007-08-06 10:25:08.000000000 +0200 +@@ -1,6 +1,7 @@ + + \documentclass{article} +-\usepackage{epsfig} ++%\usepackage{epsfig} ++\usepackage{graphicx} + + \begin{document} + \newcommand{\programtext}[1]{{\tt #1}} +@@ -707,8 +708,9 @@ + \begin{figure} + \begin{center} + \leavevmode +-\epsfxsize 300pt +-\epsfbox{genewise21.eps} ++%\epsfxsize 300pt ++%\epsfbox{genewise21.eps} ++%\includegraphics[scale=0.75]{genewise21.pdf} + \newline + \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the + arrows between them transitions. Black transitions are standard +@@ -898,8 +900,9 @@ + \begin{figure} + \begin{center} + \leavevmode +-\epsfxsize 300pt +-\epsfbox{genewise6.eps} ++%\epsfxsize 300pt ++%\epsfbox{genewise6.eps} ++%\includegraphics[scale=0.75]{genewise6.pdf} + \newline + \caption{GeneWise6:23} + \label{Figure:genewise623} Property changes on: trunk/packages/wise/trunk/debian/patches/04_wise2-pdflatex-update.patch ___________________________________________________________________ Name: svn:executable + * Name: svn:mergeinfo + Added: trunk/packages/wise/trunk/debian/patches/series =================================================================== --- trunk/packages/wise/trunk/debian/patches/series (rev 0) +++ trunk/packages/wise/trunk/debian/patches/series 2009-01-25 23:18:23 UTC (rev 3055) @@ -0,0 +1,4 @@ +01_welcome-csh.patch +02_isnumber.patch +03_doc-nodycache.patch +04_wise2-pdflatex-update.patch Modified: trunk/packages/wise/trunk/debian/rules =================================================================== --- trunk/packages/wise/trunk/debian/rules 2009-01-25 09:02:24 UTC (rev 3054) +++ trunk/packages/wise/trunk/debian/rules 2009-01-25 23:18:23 UTC (rev 3055) @@ -12,8 +12,7 @@ CFLAGS += -O2 endif -.NOTPARALLEL: -include /usr/share/dpatch/dpatch.make +include /usr/share/quilt/quilt.make configure: configure-stamp configure-stamp: @@ -22,8 +21,7 @@ touch configure-stamp build: patch build-stamp - -build-stamp: configure-stamp +build-stamp: $(QUILT_STAMPFN) configure-stamp dh_testdir $(MAKE) -C src all _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
